Multiple sequence alignment - TraesCS1D01G358500

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1D01G358500 chr1D 100.000 4778 0 0 1 4778 442329597 442334374 0.000000e+00 8824
1 TraesCS1D01G358500 chr1D 79.381 194 32 6 4537 4729 387422503 387422689 3.880000e-26 130
2 TraesCS1D01G358500 chr1B 90.446 4197 209 92 94 4184 600957098 600961208 0.000000e+00 5352
3 TraesCS1D01G358500 chr1B 94.059 303 18 0 4476 4778 600961409 600961711 1.210000e-125 460
4 TraesCS1D01G358500 chr1B 96.183 131 1 1 4169 4299 600961225 600961351 1.350000e-50 211
5 TraesCS1D01G358500 chr1B 91.892 111 8 1 4370 4480 600961347 600961456 2.300000e-33 154
6 TraesCS1D01G358500 chr1A 91.812 3896 170 67 653 4477 536356954 536353137 0.000000e+00 5289
7 TraesCS1D01G358500 chr1A 85.862 290 36 3 4481 4770 536353176 536352892 2.160000e-78 303
8 TraesCS1D01G358500 chr5D 85.161 155 11 1 1494 1648 79989927 79990069 1.070000e-31 148
9 TraesCS1D01G358500 chr5D 79.888 179 30 3 4580 4757 543832884 543833057 5.020000e-25 126
10 TraesCS1D01G358500 chr5D 79.235 183 26 11 4537 4717 400266551 400266723 3.020000e-22 117
11 TraesCS1D01G358500 chr7A 94.681 94 5 0 1553 1646 474142398 474142305 3.850000e-31 147
12 TraesCS1D01G358500 chr4B 81.356 177 25 4 4581 4757 423363606 423363774 2.320000e-28 137
13 TraesCS1D01G358500 chr4B 90.625 96 4 2 1553 1648 397267831 397267741 6.490000e-24 122
14 TraesCS1D01G358500 chr7B 93.333 90 6 0 1559 1648 532455086 532454997 3.000000e-27 134
15 TraesCS1D01G358500 chr7B 91.667 96 3 2 1553 1648 601442758 601442848 1.400000e-25 128
16 TraesCS1D01G358500 chr7B 77.064 218 40 7 4542 4757 400133422 400133631 3.020000e-22 117
17 TraesCS1D01G358500 chr7B 76.606 218 42 6 4503 4718 18225997 18226207 1.410000e-20 111
18 TraesCS1D01G358500 chr3B 91.667 96 8 0 1553 1648 290616959 290617054 3.000000e-27 134
19 TraesCS1D01G358500 chr2B 92.135 89 2 2 1560 1648 707721355 707721438 2.340000e-23 121
20 TraesCS1D01G358500 chr4A 76.389 216 39 11 4546 4757 125377671 125377464 6.540000e-19 106


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G358500 chr1D 442329597 442334374 4777 False 8824.00 8824 100.000 1 4778 1 chr1D.!!$F2 4777
1 TraesCS1D01G358500 chr1B 600957098 600961711 4613 False 1544.25 5352 93.145 94 4778 4 chr1B.!!$F1 4684
2 TraesCS1D01G358500 chr1A 536352892 536356954 4062 True 2796.00 5289 88.837 653 4770 2 chr1A.!!$R1 4117

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
396 417 0.037605 ATGAACGAACGGAGACCCAC 60.038 55.0 0.00 0.0 0.00 4.61 F
1110 1223 0.032217 AAGAGGAGGAGGAGGAGCAG 60.032 60.0 0.00 0.0 0.00 4.24 F
1923 2067 0.179045 CGGATTTGGCCTCCTCGAAT 60.179 55.0 3.32 0.0 0.00 3.34 F
2767 2937 0.109723 AGTACCACAATGTGCCCGTT 59.890 50.0 8.05 0.0 31.34 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1722 1863 0.037232 CTCCGAGTCTTTGGTGGTCC 60.037 60.0 0.00 0.00 0.00 4.46 R
2183 2330 0.109342 CACCAACCAGAGGAGCAAGT 59.891 55.0 0.00 0.00 0.00 3.16 R
3541 3711 0.396811 ACTCGAACCCCTTGTGGAAG 59.603 55.0 0.00 0.00 35.39 3.46 R
4519 4742 0.105778 CTACTAGCTGGAGCCAAGGC 59.894 60.0 3.17 2.02 43.38 4.35 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 4.329545 GGTCCGAACCAGCAGCCA 62.330 66.667 0.00 0.00 45.68 4.75
24 25 2.281484 GTCCGAACCAGCAGCCAA 60.281 61.111 0.00 0.00 0.00 4.52
25 26 1.896660 GTCCGAACCAGCAGCCAAA 60.897 57.895 0.00 0.00 0.00 3.28
26 27 1.600636 TCCGAACCAGCAGCCAAAG 60.601 57.895 0.00 0.00 0.00 2.77
27 28 1.898574 CCGAACCAGCAGCCAAAGT 60.899 57.895 0.00 0.00 0.00 2.66
28 29 0.605319 CCGAACCAGCAGCCAAAGTA 60.605 55.000 0.00 0.00 0.00 2.24
29 30 0.798776 CGAACCAGCAGCCAAAGTAG 59.201 55.000 0.00 0.00 0.00 2.57
30 31 1.608025 CGAACCAGCAGCCAAAGTAGA 60.608 52.381 0.00 0.00 0.00 2.59
31 32 2.716217 GAACCAGCAGCCAAAGTAGAT 58.284 47.619 0.00 0.00 0.00 1.98
32 33 2.409948 ACCAGCAGCCAAAGTAGATC 57.590 50.000 0.00 0.00 0.00 2.75
33 34 1.065126 ACCAGCAGCCAAAGTAGATCC 60.065 52.381 0.00 0.00 0.00 3.36
34 35 1.065199 CCAGCAGCCAAAGTAGATCCA 60.065 52.381 0.00 0.00 0.00 3.41
35 36 2.012673 CAGCAGCCAAAGTAGATCCAC 58.987 52.381 0.00 0.00 0.00 4.02
36 37 1.630369 AGCAGCCAAAGTAGATCCACA 59.370 47.619 0.00 0.00 0.00 4.17
37 38 2.240667 AGCAGCCAAAGTAGATCCACAT 59.759 45.455 0.00 0.00 0.00 3.21
38 39 3.455910 AGCAGCCAAAGTAGATCCACATA 59.544 43.478 0.00 0.00 0.00 2.29
39 40 3.561725 GCAGCCAAAGTAGATCCACATAC 59.438 47.826 0.00 0.00 0.00 2.39
40 41 4.684485 GCAGCCAAAGTAGATCCACATACT 60.684 45.833 0.00 0.00 33.67 2.12
41 42 5.453339 GCAGCCAAAGTAGATCCACATACTA 60.453 44.000 0.00 0.00 32.01 1.82
42 43 5.986135 CAGCCAAAGTAGATCCACATACTAC 59.014 44.000 0.00 0.00 37.38 2.73
43 44 5.900123 AGCCAAAGTAGATCCACATACTACT 59.100 40.000 0.00 0.00 45.47 2.57
54 55 9.427821 AGATCCACATACTACTTCTTATCAGTT 57.572 33.333 0.00 0.00 0.00 3.16
63 64 7.938715 ACTACTTCTTATCAGTTATACCACCG 58.061 38.462 0.00 0.00 0.00 4.94
64 65 7.776969 ACTACTTCTTATCAGTTATACCACCGA 59.223 37.037 0.00 0.00 0.00 4.69
65 66 6.803642 ACTTCTTATCAGTTATACCACCGAC 58.196 40.000 0.00 0.00 0.00 4.79
66 67 5.428496 TCTTATCAGTTATACCACCGACG 57.572 43.478 0.00 0.00 0.00 5.12
67 68 4.276678 TCTTATCAGTTATACCACCGACGG 59.723 45.833 13.61 13.61 0.00 4.79
68 69 1.838112 TCAGTTATACCACCGACGGT 58.162 50.000 15.37 15.37 43.46 4.83
69 70 1.745087 TCAGTTATACCACCGACGGTC 59.255 52.381 18.72 3.79 40.67 4.79
70 71 1.747355 CAGTTATACCACCGACGGTCT 59.253 52.381 18.72 6.43 40.67 3.85
71 72 2.165030 CAGTTATACCACCGACGGTCTT 59.835 50.000 18.72 9.45 40.67 3.01
72 73 3.378112 CAGTTATACCACCGACGGTCTTA 59.622 47.826 18.72 11.54 40.67 2.10
73 74 4.037208 CAGTTATACCACCGACGGTCTTAT 59.963 45.833 18.72 17.71 40.67 1.73
74 75 4.276926 AGTTATACCACCGACGGTCTTATC 59.723 45.833 18.72 5.88 40.67 1.75
75 76 2.127271 TACCACCGACGGTCTTATCA 57.873 50.000 18.72 0.00 40.67 2.15
76 77 1.481871 ACCACCGACGGTCTTATCAT 58.518 50.000 18.72 0.00 32.11 2.45
77 78 1.136305 ACCACCGACGGTCTTATCATG 59.864 52.381 18.72 2.95 32.11 3.07
78 79 1.407618 CCACCGACGGTCTTATCATGA 59.592 52.381 18.72 0.00 31.02 3.07
79 80 2.035961 CCACCGACGGTCTTATCATGAT 59.964 50.000 18.72 13.81 31.02 2.45
80 81 3.052745 CACCGACGGTCTTATCATGATG 58.947 50.000 18.72 2.44 31.02 3.07
81 82 2.956333 ACCGACGGTCTTATCATGATGA 59.044 45.455 15.37 9.32 0.00 2.92
82 83 3.383505 ACCGACGGTCTTATCATGATGAA 59.616 43.478 15.37 7.74 0.00 2.57
83 84 3.736252 CCGACGGTCTTATCATGATGAAC 59.264 47.826 18.72 9.54 0.00 3.18
84 85 3.422217 CGACGGTCTTATCATGATGAACG 59.578 47.826 24.24 24.24 44.10 3.95
85 86 4.607955 GACGGTCTTATCATGATGAACGA 58.392 43.478 29.66 11.58 41.50 3.85
86 87 5.006153 ACGGTCTTATCATGATGAACGAA 57.994 39.130 29.66 12.51 41.50 3.85
87 88 5.043903 ACGGTCTTATCATGATGAACGAAG 58.956 41.667 29.66 19.71 41.50 3.79
88 89 4.084849 CGGTCTTATCATGATGAACGAAGC 60.085 45.833 22.49 11.88 41.50 3.86
89 90 5.053145 GGTCTTATCATGATGAACGAAGCT 58.947 41.667 18.72 0.00 0.00 3.74
90 91 5.176590 GGTCTTATCATGATGAACGAAGCTC 59.823 44.000 18.72 9.19 0.00 4.09
91 92 5.750547 GTCTTATCATGATGAACGAAGCTCA 59.249 40.000 18.72 0.00 36.89 4.26
92 93 5.981915 TCTTATCATGATGAACGAAGCTCAG 59.018 40.000 18.72 0.00 35.49 3.35
97 98 0.459237 ATGAACGAAGCTCAGAGGCG 60.459 55.000 0.00 0.00 35.49 5.52
126 127 6.584942 CGTTCCTTAAATAGGGAAAAGTTTGC 59.415 38.462 5.68 0.00 42.18 3.68
127 128 7.438564 GTTCCTTAAATAGGGAAAAGTTTGCA 58.561 34.615 5.68 0.00 42.18 4.08
129 130 6.551601 TCCTTAAATAGGGAAAAGTTTGCACA 59.448 34.615 0.00 0.00 44.86 4.57
131 132 7.713073 CCTTAAATAGGGAAAAGTTTGCACAAA 59.287 33.333 0.00 0.00 40.67 2.83
132 133 8.655651 TTAAATAGGGAAAAGTTTGCACAAAG 57.344 30.769 0.00 0.00 0.00 2.77
133 134 5.869649 ATAGGGAAAAGTTTGCACAAAGT 57.130 34.783 0.00 0.00 35.61 2.66
134 135 3.860641 AGGGAAAAGTTTGCACAAAGTG 58.139 40.909 0.00 0.00 34.45 3.16
143 144 5.960113 AGTTTGCACAAAGTGAACAACATA 58.040 33.333 2.71 0.00 35.23 2.29
149 150 8.346476 TGCACAAAGTGAACAACATAATAAAC 57.654 30.769 0.58 0.00 35.23 2.01
202 204 4.702081 GCGCAGACACGACGAGGT 62.702 66.667 0.30 0.00 34.06 3.85
250 252 4.329545 GGCTCCACCGCAGTCCAA 62.330 66.667 0.00 0.00 0.00 3.53
252 254 2.425592 CTCCACCGCAGTCCAACA 59.574 61.111 0.00 0.00 0.00 3.33
254 256 0.817634 CTCCACCGCAGTCCAACAAA 60.818 55.000 0.00 0.00 0.00 2.83
255 257 1.098712 TCCACCGCAGTCCAACAAAC 61.099 55.000 0.00 0.00 0.00 2.93
256 258 1.380403 CCACCGCAGTCCAACAAACA 61.380 55.000 0.00 0.00 0.00 2.83
257 259 0.453793 CACCGCAGTCCAACAAACAA 59.546 50.000 0.00 0.00 0.00 2.83
258 260 1.135257 CACCGCAGTCCAACAAACAAA 60.135 47.619 0.00 0.00 0.00 2.83
259 261 1.135228 ACCGCAGTCCAACAAACAAAC 60.135 47.619 0.00 0.00 0.00 2.93
260 262 1.134175 CCGCAGTCCAACAAACAAACT 59.866 47.619 0.00 0.00 0.00 2.66
261 263 2.450160 CGCAGTCCAACAAACAAACTC 58.550 47.619 0.00 0.00 0.00 3.01
262 264 2.097466 CGCAGTCCAACAAACAAACTCT 59.903 45.455 0.00 0.00 0.00 3.24
263 265 3.438360 GCAGTCCAACAAACAAACTCTG 58.562 45.455 0.00 0.00 0.00 3.35
264 266 3.734902 GCAGTCCAACAAACAAACTCTGG 60.735 47.826 0.00 0.00 0.00 3.86
265 267 3.443681 CAGTCCAACAAACAAACTCTGGT 59.556 43.478 0.00 0.00 0.00 4.00
266 268 3.443681 AGTCCAACAAACAAACTCTGGTG 59.556 43.478 0.00 0.00 0.00 4.17
267 269 3.442273 GTCCAACAAACAAACTCTGGTGA 59.558 43.478 0.00 0.00 28.75 4.02
268 270 4.097892 GTCCAACAAACAAACTCTGGTGAT 59.902 41.667 0.00 0.00 28.75 3.06
269 271 4.097741 TCCAACAAACAAACTCTGGTGATG 59.902 41.667 0.00 0.00 28.75 3.07
270 272 4.142182 CCAACAAACAAACTCTGGTGATGT 60.142 41.667 0.00 0.00 28.75 3.06
271 273 4.900635 ACAAACAAACTCTGGTGATGTC 57.099 40.909 0.00 0.00 0.00 3.06
272 274 3.632145 ACAAACAAACTCTGGTGATGTCC 59.368 43.478 0.00 0.00 0.00 4.02
273 275 3.576078 AACAAACTCTGGTGATGTCCA 57.424 42.857 0.00 0.00 36.00 4.02
274 276 2.851195 ACAAACTCTGGTGATGTCCAC 58.149 47.619 0.00 0.00 44.95 4.02
275 277 1.800586 CAAACTCTGGTGATGTCCACG 59.199 52.381 0.00 0.00 46.62 4.94
276 278 0.320771 AACTCTGGTGATGTCCACGC 60.321 55.000 0.00 0.00 46.62 5.34
277 279 1.807165 CTCTGGTGATGTCCACGCG 60.807 63.158 3.53 3.53 46.62 6.01
278 280 3.490759 CTGGTGATGTCCACGCGC 61.491 66.667 5.73 0.00 46.62 6.86
293 295 4.796231 CGCGTCGGGAAGTCAGGG 62.796 72.222 2.62 0.00 0.00 4.45
296 298 3.319198 GTCGGGAAGTCAGGGCCA 61.319 66.667 6.18 0.00 0.00 5.36
299 301 2.592993 CGGGAAGTCAGGGCCAGAA 61.593 63.158 6.18 0.00 0.00 3.02
300 302 1.002011 GGGAAGTCAGGGCCAGAAC 60.002 63.158 6.18 0.00 0.00 3.01
301 303 1.761174 GGAAGTCAGGGCCAGAACA 59.239 57.895 6.18 0.00 0.00 3.18
303 305 0.687354 GAAGTCAGGGCCAGAACAGA 59.313 55.000 6.18 0.00 0.00 3.41
304 306 1.072331 GAAGTCAGGGCCAGAACAGAA 59.928 52.381 6.18 0.00 0.00 3.02
386 407 2.097728 GGCGCCGAATGAACGAAC 59.902 61.111 12.58 0.00 35.09 3.95
396 417 0.037605 ATGAACGAACGGAGACCCAC 60.038 55.000 0.00 0.00 0.00 4.61
409 430 3.324930 CCCACAGGCCAGCTGAGA 61.325 66.667 17.39 0.00 0.00 3.27
469 490 0.532862 CAAGCGTCACCACTTGGACT 60.533 55.000 1.14 0.00 39.67 3.85
473 494 1.961277 GTCACCACTTGGACTGCGG 60.961 63.158 1.14 0.00 38.94 5.69
561 591 2.355108 GGCAGATGCTAACAGGAGTGAA 60.355 50.000 4.59 0.00 41.70 3.18
567 597 2.708861 TGCTAACAGGAGTGAAAGGGAA 59.291 45.455 0.00 0.00 0.00 3.97
572 623 0.402121 AGGAGTGAAAGGGAAGCCAC 59.598 55.000 0.00 0.00 0.00 5.01
576 627 2.358247 GAAAGGGAAGCCACGCGA 60.358 61.111 15.93 0.00 0.00 5.87
592 643 2.663188 GATGATCTGGGCCGTCGC 60.663 66.667 0.00 0.00 0.00 5.19
622 673 4.107051 GTGTGCTGGATGCCGCAC 62.107 66.667 23.53 23.53 46.12 5.34
629 680 2.185867 GGATGCCGCACCGTCTAA 59.814 61.111 0.00 0.00 0.00 2.10
630 681 2.171725 GGATGCCGCACCGTCTAAC 61.172 63.158 0.00 0.00 0.00 2.34
631 682 1.447140 GATGCCGCACCGTCTAACA 60.447 57.895 0.00 0.00 0.00 2.41
632 683 1.004320 ATGCCGCACCGTCTAACAA 60.004 52.632 0.00 0.00 0.00 2.83
756 830 0.557729 AATGATAAGGGCCACCAGGG 59.442 55.000 6.18 0.00 40.13 4.45
798 872 1.948635 CAAACCAAAAGCGGCGGTG 60.949 57.895 14.17 1.78 31.94 4.94
799 873 3.783478 AAACCAAAAGCGGCGGTGC 62.783 57.895 14.17 0.00 31.94 5.01
834 912 0.106918 GTCCACACCCCACAACTTGA 60.107 55.000 0.00 0.00 0.00 3.02
851 936 1.844289 GACCCCCACCCTACACACA 60.844 63.158 0.00 0.00 0.00 3.72
852 937 2.120737 GACCCCCACCCTACACACAC 62.121 65.000 0.00 0.00 0.00 3.82
868 953 2.515991 ACACACACACCCGGCAAG 60.516 61.111 0.00 0.00 0.00 4.01
930 1015 3.721706 CTCCCCTCCCCACTGTGC 61.722 72.222 1.29 0.00 0.00 4.57
957 1046 2.978946 GCCCGTTCATTCCCTCCCA 61.979 63.158 0.00 0.00 0.00 4.37
958 1047 1.922821 CCCGTTCATTCCCTCCCAT 59.077 57.895 0.00 0.00 0.00 4.00
959 1048 0.179018 CCCGTTCATTCCCTCCCATC 60.179 60.000 0.00 0.00 0.00 3.51
960 1049 0.179018 CCGTTCATTCCCTCCCATCC 60.179 60.000 0.00 0.00 0.00 3.51
961 1050 0.179018 CGTTCATTCCCTCCCATCCC 60.179 60.000 0.00 0.00 0.00 3.85
972 1061 3.081409 CCATCCCCGGTTCCGTCT 61.081 66.667 10.36 0.00 0.00 4.18
1059 1156 3.382803 CTCCCTCTTCTGCTGCCCG 62.383 68.421 0.00 0.00 0.00 6.13
1105 1218 0.467290 CGAGGAAGAGGAGGAGGAGG 60.467 65.000 0.00 0.00 0.00 4.30
1106 1219 0.930726 GAGGAAGAGGAGGAGGAGGA 59.069 60.000 0.00 0.00 0.00 3.71
1107 1220 0.933700 AGGAAGAGGAGGAGGAGGAG 59.066 60.000 0.00 0.00 0.00 3.69
1108 1221 0.759060 GGAAGAGGAGGAGGAGGAGC 60.759 65.000 0.00 0.00 0.00 4.70
1109 1222 0.032615 GAAGAGGAGGAGGAGGAGCA 60.033 60.000 0.00 0.00 0.00 4.26
1110 1223 0.032217 AAGAGGAGGAGGAGGAGCAG 60.032 60.000 0.00 0.00 0.00 4.24
1111 1224 1.457455 GAGGAGGAGGAGGAGCAGG 60.457 68.421 0.00 0.00 0.00 4.85
1112 1225 1.938596 AGGAGGAGGAGGAGCAGGA 60.939 63.158 0.00 0.00 0.00 3.86
1303 1416 4.649310 TACGCACGCCGCACTCAA 62.649 61.111 0.00 0.00 42.60 3.02
1307 1420 2.967076 CACGCCGCACTCAACACT 60.967 61.111 0.00 0.00 0.00 3.55
1308 1421 2.661866 ACGCCGCACTCAACACTC 60.662 61.111 0.00 0.00 0.00 3.51
1309 1422 2.661537 CGCCGCACTCAACACTCA 60.662 61.111 0.00 0.00 0.00 3.41
1310 1423 2.939022 GCCGCACTCAACACTCAC 59.061 61.111 0.00 0.00 0.00 3.51
1311 1424 2.607892 GCCGCACTCAACACTCACC 61.608 63.158 0.00 0.00 0.00 4.02
1312 1425 1.961277 CCGCACTCAACACTCACCC 60.961 63.158 0.00 0.00 0.00 4.61
1313 1426 1.069765 CGCACTCAACACTCACCCT 59.930 57.895 0.00 0.00 0.00 4.34
1314 1427 0.946221 CGCACTCAACACTCACCCTC 60.946 60.000 0.00 0.00 0.00 4.30
1348 1461 4.986783 TCCTTTCTTTCTTTCCTCCTTCC 58.013 43.478 0.00 0.00 0.00 3.46
1601 1721 1.441515 CGACTTCGAAGACGCCGAA 60.442 57.895 30.52 0.00 42.79 4.30
1618 1750 1.950909 CGAAGCCAACACCAAAGGTTA 59.049 47.619 0.00 0.00 31.02 2.85
1619 1751 2.359531 CGAAGCCAACACCAAAGGTTAA 59.640 45.455 0.00 0.00 31.02 2.01
1620 1752 3.005367 CGAAGCCAACACCAAAGGTTAAT 59.995 43.478 0.00 0.00 31.02 1.40
1621 1753 4.500716 CGAAGCCAACACCAAAGGTTAATT 60.501 41.667 0.00 0.00 31.02 1.40
1722 1863 3.432051 GATGTCCCTCGGCGACAGG 62.432 68.421 4.99 10.47 43.17 4.00
1812 1956 3.562732 AACCCCGGCTGTTAGGTGC 62.563 63.158 5.86 0.00 31.45 5.01
1875 2019 1.152963 ACCGAGCTTGTTGCCTTGT 60.153 52.632 0.00 0.00 44.23 3.16
1919 2063 1.657751 GCAACGGATTTGGCCTCCTC 61.658 60.000 3.32 0.00 35.51 3.71
1923 2067 0.179045 CGGATTTGGCCTCCTCGAAT 60.179 55.000 3.32 0.00 0.00 3.34
1945 2089 2.227388 CGATGCTCAACTTCCTGCTTTT 59.773 45.455 0.00 0.00 0.00 2.27
1948 2092 2.760092 TGCTCAACTTCCTGCTTTTTGT 59.240 40.909 0.00 0.00 0.00 2.83
1952 2096 3.509575 TCAACTTCCTGCTTTTTGTGTGT 59.490 39.130 0.00 0.00 0.00 3.72
1953 2097 3.782889 ACTTCCTGCTTTTTGTGTGTC 57.217 42.857 0.00 0.00 0.00 3.67
1975 2119 6.016610 TGTCAACTTTACCATCTTTTAGGCAC 60.017 38.462 0.00 0.00 0.00 5.01
2033 2180 2.995574 ACCCTCCCAACCGTCTCG 60.996 66.667 0.00 0.00 0.00 4.04
2126 2273 4.207891 TCTCATGTTTCTTGGTCTAGCC 57.792 45.455 0.00 0.00 37.90 3.93
2149 2296 6.090129 CCGTTGGTAATTAGGTGTTTGATTG 58.910 40.000 0.00 0.00 0.00 2.67
2191 2338 3.933332 GTGTGATGGTACTTACTTGCTCC 59.067 47.826 0.00 0.00 0.00 4.70
2200 2369 2.039084 ACTTACTTGCTCCTCTGGTTGG 59.961 50.000 0.00 0.00 0.00 3.77
2288 2457 3.570926 TCTCAGCAACAAGGTAGTACG 57.429 47.619 0.00 0.00 0.00 3.67
2293 2462 6.028146 TCAGCAACAAGGTAGTACGAAATA 57.972 37.500 0.00 0.00 0.00 1.40
2362 2531 5.596361 TCTGCTGGTTTTGTTCCTAATTCAA 59.404 36.000 0.00 0.00 0.00 2.69
2393 2562 8.037758 CACTGTTCTATTGAGTCATCTTTAGGT 58.962 37.037 0.00 0.00 0.00 3.08
2399 2568 8.206867 TCTATTGAGTCATCTTTAGGTTGATGG 58.793 37.037 0.00 0.00 40.13 3.51
2429 2598 5.434352 GCACATCTGCAATGAGATATTGT 57.566 39.130 13.53 0.00 43.62 2.71
2452 2621 6.707608 TGTCATATGCATATGTCCAACTCTTC 59.292 38.462 34.65 18.17 40.69 2.87
2593 2763 1.616725 GGCAACATCAGGATTCACCCA 60.617 52.381 0.00 0.00 40.05 4.51
2641 2811 2.224967 ACCTGCCAGCTCAAAGAGAAAT 60.225 45.455 0.00 0.00 0.00 2.17
2659 2829 6.772716 AGAGAAATGAGCTGTGGAAACTTAAA 59.227 34.615 0.00 0.00 0.00 1.52
2683 2853 3.449737 CCTACCCTCGTAAAGGTGATGAA 59.550 47.826 0.00 0.00 44.56 2.57
2767 2937 0.109723 AGTACCACAATGTGCCCGTT 59.890 50.000 8.05 0.00 31.34 4.44
2851 3021 1.006102 CCTCTTCACGACGGCAAGT 60.006 57.895 0.00 0.00 0.00 3.16
2869 3039 1.072331 AGTGAGTTCAATGGCGAGGTT 59.928 47.619 0.00 0.00 0.00 3.50
2872 3042 2.151202 GAGTTCAATGGCGAGGTTCAA 58.849 47.619 0.00 0.00 0.00 2.69
2953 3123 4.827789 AGCTATCCAACTACCCCTTGATA 58.172 43.478 0.00 0.00 0.00 2.15
3259 3429 2.027625 CGTGGTCGAGGAAGCCAAC 61.028 63.158 0.00 0.00 39.71 3.77
3301 3471 1.056660 TCTCCAAGGTGGTGAACTCC 58.943 55.000 0.00 0.00 37.12 3.85
3304 3474 0.602905 CCAAGGTGGTGAACTCCGTC 60.603 60.000 0.00 0.00 37.80 4.79
3307 3477 1.372623 GGTGGTGAACTCCGTCGAC 60.373 63.158 5.18 5.18 0.00 4.20
3541 3711 2.282180 TTCAAGAACCCGCTGGCC 60.282 61.111 0.00 0.00 33.59 5.36
3618 3788 1.021202 CTTGACTGCAACCGGTTCAA 58.979 50.000 19.24 17.18 0.00 2.69
3964 4145 4.321008 GGCATGGAAATATCAGTGCATGAG 60.321 45.833 15.32 0.00 42.53 2.90
3998 4179 2.611518 GTCAGTGAGGAGGAATGTTCG 58.388 52.381 0.00 0.00 0.00 3.95
4167 4349 6.326323 TGACCAGGCCTCTTTCTTTTATTTTT 59.674 34.615 0.00 0.00 0.00 1.94
4333 4548 4.057432 AGCACATATGTTTTGTTGTTGGC 58.943 39.130 5.37 2.49 0.00 4.52
4349 4564 6.544197 TGTTGTTGGCTAGTCAACTCAAATAA 59.456 34.615 33.51 19.50 45.15 1.40
4350 4565 6.554334 TGTTGGCTAGTCAACTCAAATAAC 57.446 37.500 33.51 11.67 45.15 1.89
4351 4566 5.472137 TGTTGGCTAGTCAACTCAAATAACC 59.528 40.000 33.51 10.26 45.15 2.85
4480 4703 1.002134 AGTGAAATCCTGGTGCCCG 60.002 57.895 0.00 0.00 0.00 6.13
4481 4704 1.303317 GTGAAATCCTGGTGCCCGT 60.303 57.895 0.00 0.00 0.00 5.28
4482 4705 1.002624 TGAAATCCTGGTGCCCGTC 60.003 57.895 0.00 0.00 0.00 4.79
4483 4706 2.046314 AAATCCTGGTGCCCGTCG 60.046 61.111 0.00 0.00 0.00 5.12
4484 4707 4.778143 AATCCTGGTGCCCGTCGC 62.778 66.667 0.00 0.00 38.31 5.19
4496 4719 4.778415 CGTCGCTCCGTCACCCAG 62.778 72.222 0.00 0.00 0.00 4.45
4500 4723 4.148825 GCTCCGTCACCCAGCGAT 62.149 66.667 0.00 0.00 0.00 4.58
4501 4724 2.202797 CTCCGTCACCCAGCGATG 60.203 66.667 0.00 0.00 0.00 3.84
4502 4725 3.723235 CTCCGTCACCCAGCGATGG 62.723 68.421 14.18 14.18 40.38 3.51
4510 4733 2.989639 CCAGCGATGGGGAGTGAA 59.010 61.111 13.14 0.00 0.00 3.18
4511 4734 1.299648 CCAGCGATGGGGAGTGAAA 59.700 57.895 13.14 0.00 0.00 2.69
4512 4735 0.107017 CCAGCGATGGGGAGTGAAAT 60.107 55.000 13.14 0.00 0.00 2.17
4513 4736 1.303309 CAGCGATGGGGAGTGAAATC 58.697 55.000 0.00 0.00 0.00 2.17
4514 4737 0.181350 AGCGATGGGGAGTGAAATCC 59.819 55.000 0.00 0.00 38.76 3.01
4515 4738 0.181350 GCGATGGGGAGTGAAATCCT 59.819 55.000 0.00 0.00 39.50 3.24
4516 4739 1.959042 CGATGGGGAGTGAAATCCTG 58.041 55.000 0.00 0.00 39.50 3.86
4517 4740 1.475751 CGATGGGGAGTGAAATCCTGG 60.476 57.143 0.00 0.00 39.50 4.45
4518 4741 1.566231 GATGGGGAGTGAAATCCTGGT 59.434 52.381 0.00 0.00 39.50 4.00
4519 4742 0.698238 TGGGGAGTGAAATCCTGGTG 59.302 55.000 0.00 0.00 39.50 4.17
4520 4743 0.681243 GGGGAGTGAAATCCTGGTGC 60.681 60.000 0.00 0.00 39.50 5.01
4521 4744 0.681243 GGGAGTGAAATCCTGGTGCC 60.681 60.000 0.00 0.00 39.50 5.01
4522 4745 0.329596 GGAGTGAAATCCTGGTGCCT 59.670 55.000 0.00 0.00 36.35 4.75
4523 4746 1.272147 GGAGTGAAATCCTGGTGCCTT 60.272 52.381 0.00 0.00 36.35 4.35
4664 4887 6.068670 TGTCGGGACAGATTAGATTAGATGA 58.931 40.000 0.00 0.00 36.21 2.92
4688 4911 0.389391 CCGACATAGATTCCTGCCGT 59.611 55.000 0.00 0.00 0.00 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.046285 GCTGGTTCGGACCCCATTG 61.046 63.158 11.33 0.00 45.92 2.82
1 2 2.355115 GCTGGTTCGGACCCCATT 59.645 61.111 11.33 0.00 45.92 3.16
2 3 2.933287 TGCTGGTTCGGACCCCAT 60.933 61.111 11.33 0.00 45.92 4.00
3 4 3.636231 CTGCTGGTTCGGACCCCA 61.636 66.667 11.33 6.80 45.92 4.96
6 7 3.842925 TTGGCTGCTGGTTCGGACC 62.843 63.158 5.70 5.70 46.71 4.46
7 8 1.856265 CTTTGGCTGCTGGTTCGGAC 61.856 60.000 0.00 0.00 0.00 4.79
8 9 1.600636 CTTTGGCTGCTGGTTCGGA 60.601 57.895 0.00 0.00 0.00 4.55
9 10 0.605319 TACTTTGGCTGCTGGTTCGG 60.605 55.000 0.00 0.00 0.00 4.30
10 11 0.798776 CTACTTTGGCTGCTGGTTCG 59.201 55.000 0.00 0.00 0.00 3.95
11 12 2.185004 TCTACTTTGGCTGCTGGTTC 57.815 50.000 0.00 0.00 0.00 3.62
12 13 2.619074 GGATCTACTTTGGCTGCTGGTT 60.619 50.000 0.00 0.00 0.00 3.67
13 14 1.065126 GGATCTACTTTGGCTGCTGGT 60.065 52.381 0.00 0.00 0.00 4.00
14 15 1.065199 TGGATCTACTTTGGCTGCTGG 60.065 52.381 0.00 0.00 0.00 4.85
15 16 2.012673 GTGGATCTACTTTGGCTGCTG 58.987 52.381 1.27 0.00 0.00 4.41
16 17 1.630369 TGTGGATCTACTTTGGCTGCT 59.370 47.619 10.82 0.00 0.00 4.24
17 18 2.113860 TGTGGATCTACTTTGGCTGC 57.886 50.000 10.82 0.00 0.00 5.25
18 19 5.028549 AGTATGTGGATCTACTTTGGCTG 57.971 43.478 10.82 0.00 0.00 4.85
19 20 5.900123 AGTAGTATGTGGATCTACTTTGGCT 59.100 40.000 10.82 6.34 40.63 4.75
20 21 6.163135 AGTAGTATGTGGATCTACTTTGGC 57.837 41.667 10.82 0.00 40.63 4.52
28 29 9.427821 AACTGATAAGAAGTAGTATGTGGATCT 57.572 33.333 0.00 0.00 0.00 2.75
37 38 9.060347 CGGTGGTATAACTGATAAGAAGTAGTA 57.940 37.037 0.00 0.00 0.00 1.82
38 39 7.776969 TCGGTGGTATAACTGATAAGAAGTAGT 59.223 37.037 0.00 0.00 30.36 2.73
39 40 8.074972 GTCGGTGGTATAACTGATAAGAAGTAG 58.925 40.741 0.00 0.00 37.75 2.57
40 41 7.254898 CGTCGGTGGTATAACTGATAAGAAGTA 60.255 40.741 0.00 0.00 37.75 2.24
41 42 6.459298 CGTCGGTGGTATAACTGATAAGAAGT 60.459 42.308 0.00 0.00 37.75 3.01
42 43 5.913514 CGTCGGTGGTATAACTGATAAGAAG 59.086 44.000 0.00 0.00 37.75 2.85
43 44 5.221106 CCGTCGGTGGTATAACTGATAAGAA 60.221 44.000 2.08 0.00 37.75 2.52
44 45 4.276678 CCGTCGGTGGTATAACTGATAAGA 59.723 45.833 2.08 0.00 37.75 2.10
45 46 4.037208 ACCGTCGGTGGTATAACTGATAAG 59.963 45.833 18.08 0.00 41.55 1.73
46 47 3.953612 ACCGTCGGTGGTATAACTGATAA 59.046 43.478 18.08 0.00 41.55 1.75
47 48 3.554934 ACCGTCGGTGGTATAACTGATA 58.445 45.455 18.08 0.00 41.55 2.15
48 49 2.360165 GACCGTCGGTGGTATAACTGAT 59.640 50.000 24.45 0.00 44.01 2.90
49 50 1.745087 GACCGTCGGTGGTATAACTGA 59.255 52.381 24.45 0.00 44.01 3.41
50 51 1.747355 AGACCGTCGGTGGTATAACTG 59.253 52.381 24.45 0.00 44.01 3.16
51 52 2.134789 AGACCGTCGGTGGTATAACT 57.865 50.000 24.45 7.75 44.01 2.24
52 53 2.947448 AAGACCGTCGGTGGTATAAC 57.053 50.000 24.45 5.16 44.01 1.89
53 54 4.206375 TGATAAGACCGTCGGTGGTATAA 58.794 43.478 24.45 9.14 44.01 0.98
54 55 3.819368 TGATAAGACCGTCGGTGGTATA 58.181 45.455 24.45 9.41 44.01 1.47
55 56 2.658285 TGATAAGACCGTCGGTGGTAT 58.342 47.619 24.45 17.86 44.01 2.73
56 57 2.127271 TGATAAGACCGTCGGTGGTA 57.873 50.000 24.45 13.68 44.01 3.25
58 59 1.407618 TCATGATAAGACCGTCGGTGG 59.592 52.381 24.45 0.89 35.25 4.61
59 60 2.863401 TCATGATAAGACCGTCGGTG 57.137 50.000 24.45 4.63 35.25 4.94
60 61 2.956333 TCATCATGATAAGACCGTCGGT 59.044 45.455 18.94 18.94 39.44 4.69
61 62 3.643159 TCATCATGATAAGACCGTCGG 57.357 47.619 10.48 10.48 0.00 4.79
62 63 3.422217 CGTTCATCATGATAAGACCGTCG 59.578 47.826 8.15 2.06 0.00 5.12
63 64 4.607955 TCGTTCATCATGATAAGACCGTC 58.392 43.478 8.15 0.00 0.00 4.79
64 65 4.649088 TCGTTCATCATGATAAGACCGT 57.351 40.909 8.15 0.00 0.00 4.83
65 66 4.084849 GCTTCGTTCATCATGATAAGACCG 60.085 45.833 16.08 11.48 0.00 4.79
66 67 5.053145 AGCTTCGTTCATCATGATAAGACC 58.947 41.667 16.08 1.02 0.00 3.85
67 68 5.750547 TGAGCTTCGTTCATCATGATAAGAC 59.249 40.000 16.08 10.75 0.00 3.01
68 69 5.906073 TGAGCTTCGTTCATCATGATAAGA 58.094 37.500 16.08 5.65 0.00 2.10
69 70 5.981915 TCTGAGCTTCGTTCATCATGATAAG 59.018 40.000 8.15 9.16 0.00 1.73
70 71 5.906073 TCTGAGCTTCGTTCATCATGATAA 58.094 37.500 8.15 0.00 0.00 1.75
71 72 5.508657 CCTCTGAGCTTCGTTCATCATGATA 60.509 44.000 8.15 0.00 0.00 2.15
72 73 4.370049 CTCTGAGCTTCGTTCATCATGAT 58.630 43.478 1.18 1.18 0.00 2.45
73 74 3.429960 CCTCTGAGCTTCGTTCATCATGA 60.430 47.826 0.00 0.00 0.00 3.07
74 75 2.864946 CCTCTGAGCTTCGTTCATCATG 59.135 50.000 0.00 0.00 0.00 3.07
75 76 2.741228 GCCTCTGAGCTTCGTTCATCAT 60.741 50.000 0.00 0.00 0.00 2.45
76 77 1.404717 GCCTCTGAGCTTCGTTCATCA 60.405 52.381 0.00 0.00 0.00 3.07
77 78 1.285578 GCCTCTGAGCTTCGTTCATC 58.714 55.000 0.00 0.00 0.00 2.92
78 79 0.459237 CGCCTCTGAGCTTCGTTCAT 60.459 55.000 0.00 0.00 0.00 2.57
79 80 1.080501 CGCCTCTGAGCTTCGTTCA 60.081 57.895 0.00 0.00 0.00 3.18
80 81 1.807573 CCGCCTCTGAGCTTCGTTC 60.808 63.158 0.00 0.00 0.00 3.95
81 82 2.262915 CCGCCTCTGAGCTTCGTT 59.737 61.111 0.00 0.00 0.00 3.85
82 83 4.443266 GCCGCCTCTGAGCTTCGT 62.443 66.667 0.00 0.00 0.00 3.85
83 84 4.441695 TGCCGCCTCTGAGCTTCG 62.442 66.667 0.00 2.52 0.00 3.79
84 85 2.817396 GTGCCGCCTCTGAGCTTC 60.817 66.667 0.00 0.00 0.00 3.86
85 86 4.749310 CGTGCCGCCTCTGAGCTT 62.749 66.667 0.00 0.00 0.00 3.74
88 89 2.811317 GAACGTGCCGCCTCTGAG 60.811 66.667 0.00 0.00 0.00 3.35
89 90 4.373116 GGAACGTGCCGCCTCTGA 62.373 66.667 0.00 0.00 0.00 3.27
90 91 2.501223 TAAGGAACGTGCCGCCTCTG 62.501 60.000 7.01 0.00 0.00 3.35
91 92 1.823169 TTAAGGAACGTGCCGCCTCT 61.823 55.000 7.01 0.00 0.00 3.69
92 93 0.952010 TTTAAGGAACGTGCCGCCTC 60.952 55.000 7.01 0.00 0.00 4.70
107 108 8.261522 ACTTTGTGCAAACTTTTCCCTATTTAA 58.738 29.630 0.00 0.00 0.00 1.52
108 109 7.708752 CACTTTGTGCAAACTTTTCCCTATTTA 59.291 33.333 0.00 0.00 0.00 1.40
112 113 4.707448 TCACTTTGTGCAAACTTTTCCCTA 59.293 37.500 0.00 0.00 32.98 3.53
113 114 3.513515 TCACTTTGTGCAAACTTTTCCCT 59.486 39.130 0.00 0.00 32.98 4.20
126 127 7.646130 ACGGTTTATTATGTTGTTCACTTTGTG 59.354 33.333 0.00 0.00 34.45 3.33
127 128 7.708998 ACGGTTTATTATGTTGTTCACTTTGT 58.291 30.769 0.00 0.00 0.00 2.83
129 130 8.568732 CAACGGTTTATTATGTTGTTCACTTT 57.431 30.769 0.00 0.00 37.51 2.66
162 163 2.485122 CGCGCCTTTGGATTGGAC 59.515 61.111 0.00 0.00 0.00 4.02
186 188 1.213094 AAAACCTCGTCGTGTCTGCG 61.213 55.000 0.00 0.00 0.00 5.18
189 191 0.935196 GCAAAAACCTCGTCGTGTCT 59.065 50.000 0.00 0.00 0.00 3.41
190 192 0.935196 AGCAAAAACCTCGTCGTGTC 59.065 50.000 0.00 0.00 0.00 3.67
250 252 3.632145 GGACATCACCAGAGTTTGTTTGT 59.368 43.478 0.00 0.00 0.00 2.83
252 254 3.632145 GTGGACATCACCAGAGTTTGTTT 59.368 43.478 0.00 0.00 40.85 2.83
254 256 2.806745 CGTGGACATCACCAGAGTTTGT 60.807 50.000 0.00 0.00 43.23 2.83
255 257 1.800586 CGTGGACATCACCAGAGTTTG 59.199 52.381 0.00 0.00 43.23 2.93
256 258 1.878102 GCGTGGACATCACCAGAGTTT 60.878 52.381 0.00 0.00 43.23 2.66
257 259 0.320771 GCGTGGACATCACCAGAGTT 60.321 55.000 0.00 0.00 43.23 3.01
258 260 1.293498 GCGTGGACATCACCAGAGT 59.707 57.895 0.00 0.00 43.23 3.24
259 261 1.807165 CGCGTGGACATCACCAGAG 60.807 63.158 0.00 0.00 43.23 3.35
260 262 2.261361 CGCGTGGACATCACCAGA 59.739 61.111 0.00 0.00 43.23 3.86
261 263 3.490759 GCGCGTGGACATCACCAG 61.491 66.667 8.43 0.00 43.23 4.00
264 266 3.838795 GACGCGCGTGGACATCAC 61.839 66.667 42.90 19.75 42.74 3.06
276 278 4.796231 CCCTGACTTCCCGACGCG 62.796 72.222 3.53 3.53 0.00 6.01
278 280 4.452733 GGCCCTGACTTCCCGACG 62.453 72.222 0.00 0.00 0.00 5.12
279 281 3.316573 CTGGCCCTGACTTCCCGAC 62.317 68.421 0.00 0.00 0.00 4.79
284 286 0.687354 TCTGTTCTGGCCCTGACTTC 59.313 55.000 0.00 0.00 0.00 3.01
293 295 3.793144 CCGCGCTTCTGTTCTGGC 61.793 66.667 5.56 0.00 0.00 4.85
296 298 4.664677 ACGCCGCGCTTCTGTTCT 62.665 61.111 13.88 0.00 0.00 3.01
299 301 4.742201 ATCACGCCGCGCTTCTGT 62.742 61.111 13.88 0.00 0.00 3.41
300 302 3.918220 GATCACGCCGCGCTTCTG 61.918 66.667 13.88 3.49 0.00 3.02
376 397 0.682852 TGGGTCTCCGTTCGTTCATT 59.317 50.000 0.00 0.00 35.24 2.57
386 407 4.087892 CTGGCCTGTGGGTCTCCG 62.088 72.222 3.32 0.00 38.23 4.63
396 417 0.759959 ATCTCATCTCAGCTGGCCTG 59.240 55.000 15.13 4.26 43.17 4.85
409 430 1.476085 GCCGATCAGATCCGATCTCAT 59.524 52.381 15.33 0.58 39.78 2.90
461 482 2.345244 CTCTGCCGCAGTCCAAGT 59.655 61.111 19.77 0.00 32.61 3.16
473 494 4.537433 AATCCCGCTCGCCTCTGC 62.537 66.667 0.00 0.00 0.00 4.26
548 571 3.339141 GCTTCCCTTTCACTCCTGTTAG 58.661 50.000 0.00 0.00 0.00 2.34
561 591 2.257409 ATCATCGCGTGGCTTCCCTT 62.257 55.000 5.77 0.00 0.00 3.95
567 597 2.107750 CCAGATCATCGCGTGGCT 59.892 61.111 5.77 2.95 0.00 4.75
572 623 4.592192 ACGGCCCAGATCATCGCG 62.592 66.667 0.00 0.00 0.00 5.87
576 627 3.157217 GAGCGACGGCCCAGATCAT 62.157 63.158 0.00 0.00 41.24 2.45
614 665 1.004320 TTGTTAGACGGTGCGGCAT 60.004 52.632 5.72 0.00 37.34 4.40
615 666 1.666553 CTTGTTAGACGGTGCGGCA 60.667 57.895 0.00 0.00 37.34 5.69
626 677 2.621526 AGAAAAACCACCGGCTTGTTAG 59.378 45.455 0.00 0.00 0.00 2.34
629 680 2.227194 CTAGAAAAACCACCGGCTTGT 58.773 47.619 0.00 0.00 0.00 3.16
630 681 2.227194 ACTAGAAAAACCACCGGCTTG 58.773 47.619 0.00 0.00 0.00 4.01
631 682 2.651382 ACTAGAAAAACCACCGGCTT 57.349 45.000 0.00 0.00 0.00 4.35
632 683 2.636403 ACTACTAGAAAAACCACCGGCT 59.364 45.455 0.00 0.00 0.00 5.52
673 743 8.462016 CGTCTCCTCTCCAAAAATTAAATTGAT 58.538 33.333 1.34 0.00 0.00 2.57
674 744 7.663905 TCGTCTCCTCTCCAAAAATTAAATTGA 59.336 33.333 1.34 0.00 0.00 2.57
675 745 7.816640 TCGTCTCCTCTCCAAAAATTAAATTG 58.183 34.615 0.00 0.00 0.00 2.32
676 746 7.121315 CCTCGTCTCCTCTCCAAAAATTAAATT 59.879 37.037 0.00 0.00 0.00 1.82
756 830 2.994671 GCAGCTTTCCTTTCCCGGC 61.995 63.158 0.00 0.00 0.00 6.13
834 912 2.151388 GTGTGTGTAGGGTGGGGGT 61.151 63.158 0.00 0.00 0.00 4.95
851 936 2.515991 CTTGCCGGGTGTGTGTGT 60.516 61.111 2.18 0.00 0.00 3.72
852 937 2.203139 TCTTGCCGGGTGTGTGTG 60.203 61.111 2.18 0.00 0.00 3.82
868 953 0.037512 TGCTCTGCTCTGCTCTTGTC 60.038 55.000 0.00 0.00 0.00 3.18
930 1015 2.826777 AATGAACGGGCAGAGGCAGG 62.827 60.000 0.00 0.00 43.71 4.85
957 1046 2.284405 ACAGACGGAACCGGGGAT 60.284 61.111 17.44 0.00 44.69 3.85
958 1047 2.993264 GACAGACGGAACCGGGGA 60.993 66.667 17.44 0.00 44.69 4.81
959 1048 4.078516 GGACAGACGGAACCGGGG 62.079 72.222 17.44 8.53 44.69 5.73
960 1049 4.078516 GGGACAGACGGAACCGGG 62.079 72.222 17.44 8.86 44.69 5.73
961 1050 4.078516 GGGGACAGACGGAACCGG 62.079 72.222 17.44 0.00 44.69 5.28
972 1061 4.631740 TGGAGCTCGGTGGGGACA 62.632 66.667 7.83 0.00 38.70 4.02
1059 1156 2.594013 GGCTGGCTGGCTAGATGC 60.594 66.667 10.05 0.84 41.94 3.91
1060 1157 1.227883 CTGGCTGGCTGGCTAGATG 60.228 63.158 18.27 0.00 42.23 2.90
1061 1158 3.117452 GCTGGCTGGCTGGCTAGAT 62.117 63.158 18.27 0.00 42.23 1.98
1062 1159 3.790437 GCTGGCTGGCTGGCTAGA 61.790 66.667 18.27 0.00 42.23 2.43
1105 1218 2.041265 TCCTTCCCCCTCCTGCTC 59.959 66.667 0.00 0.00 0.00 4.26
1106 1219 2.041928 CTCCTTCCCCCTCCTGCT 59.958 66.667 0.00 0.00 0.00 4.24
1107 1220 3.093172 CCTCCTTCCCCCTCCTGC 61.093 72.222 0.00 0.00 0.00 4.85
1108 1221 2.277126 ATCCCTCCTTCCCCCTCCTG 62.277 65.000 0.00 0.00 0.00 3.86
1109 1222 1.954994 ATCCCTCCTTCCCCCTCCT 60.955 63.158 0.00 0.00 0.00 3.69
1110 1223 1.462432 GATCCCTCCTTCCCCCTCC 60.462 68.421 0.00 0.00 0.00 4.30
1111 1224 1.839296 CGATCCCTCCTTCCCCCTC 60.839 68.421 0.00 0.00 0.00 4.30
1112 1225 2.287251 CGATCCCTCCTTCCCCCT 59.713 66.667 0.00 0.00 0.00 4.79
1303 1416 1.645710 AAGAATCGGAGGGTGAGTGT 58.354 50.000 0.00 0.00 0.00 3.55
1305 1418 2.541466 AGAAAGAATCGGAGGGTGAGT 58.459 47.619 0.00 0.00 0.00 3.41
1307 1420 2.236395 GGAAGAAAGAATCGGAGGGTGA 59.764 50.000 0.00 0.00 0.00 4.02
1308 1421 2.237392 AGGAAGAAAGAATCGGAGGGTG 59.763 50.000 0.00 0.00 0.00 4.61
1309 1422 2.552367 AGGAAGAAAGAATCGGAGGGT 58.448 47.619 0.00 0.00 0.00 4.34
1310 1423 3.636153 AAGGAAGAAAGAATCGGAGGG 57.364 47.619 0.00 0.00 0.00 4.30
1311 1424 4.837972 AGAAAGGAAGAAAGAATCGGAGG 58.162 43.478 0.00 0.00 0.00 4.30
1312 1425 6.652900 AGAAAGAAAGGAAGAAAGAATCGGAG 59.347 38.462 0.00 0.00 0.00 4.63
1313 1426 6.534634 AGAAAGAAAGGAAGAAAGAATCGGA 58.465 36.000 0.00 0.00 0.00 4.55
1314 1427 6.809630 AGAAAGAAAGGAAGAAAGAATCGG 57.190 37.500 0.00 0.00 0.00 4.18
1348 1461 5.636543 GGTTGCAAGAAGGAAATGAAGAATG 59.363 40.000 0.00 0.00 0.00 2.67
1560 1680 4.366684 CACCTTGGGGTCCTGGGC 62.367 72.222 0.00 0.00 45.41 5.36
1561 1681 4.366684 GCACCTTGGGGTCCTGGG 62.367 72.222 0.00 0.00 45.41 4.45
1562 1682 3.260100 AGCACCTTGGGGTCCTGG 61.260 66.667 0.00 0.00 45.41 4.45
1575 1695 0.039437 TCTTCGAAGTCGTCCAGCAC 60.039 55.000 23.85 0.00 40.80 4.40
1576 1696 0.039437 GTCTTCGAAGTCGTCCAGCA 60.039 55.000 23.85 0.00 40.80 4.41
1601 1721 4.282449 GGTAATTAACCTTTGGTGTTGGCT 59.718 41.667 0.00 0.00 45.75 4.75
1618 1750 6.155049 CAGGATTTGATTTGGAGGTGGTAATT 59.845 38.462 0.00 0.00 0.00 1.40
1619 1751 5.658190 CAGGATTTGATTTGGAGGTGGTAAT 59.342 40.000 0.00 0.00 0.00 1.89
1620 1752 5.016173 CAGGATTTGATTTGGAGGTGGTAA 58.984 41.667 0.00 0.00 0.00 2.85
1621 1753 4.569653 CCAGGATTTGATTTGGAGGTGGTA 60.570 45.833 0.00 0.00 32.34 3.25
1665 1804 8.777578 TCCAAGATAAAATAGTACTGCTAGGA 57.222 34.615 5.39 0.00 32.45 2.94
1722 1863 0.037232 CTCCGAGTCTTTGGTGGTCC 60.037 60.000 0.00 0.00 0.00 4.46
1919 2063 2.283617 CAGGAAGTTGAGCATCGATTCG 59.716 50.000 0.00 0.00 38.61 3.34
1923 2067 0.610174 AGCAGGAAGTTGAGCATCGA 59.390 50.000 0.00 0.00 38.61 3.59
1945 2089 6.767524 AAAGATGGTAAAGTTGACACACAA 57.232 33.333 0.00 0.00 36.02 3.33
1948 2092 6.016610 GCCTAAAAGATGGTAAAGTTGACACA 60.017 38.462 0.00 0.00 0.00 3.72
1952 2096 6.303839 AGTGCCTAAAAGATGGTAAAGTTGA 58.696 36.000 0.00 0.00 0.00 3.18
1953 2097 6.575162 AGTGCCTAAAAGATGGTAAAGTTG 57.425 37.500 0.00 0.00 0.00 3.16
1975 2119 1.007238 TCTCCCCTTCACCTCCACTAG 59.993 57.143 0.00 0.00 0.00 2.57
2033 2180 2.391879 GCGTCACGGATGGTATAGTTC 58.608 52.381 0.00 0.00 0.00 3.01
2126 2273 6.072397 TCCAATCAAACACCTAATTACCAACG 60.072 38.462 0.00 0.00 0.00 4.10
2167 2314 5.228945 AGCAAGTAAGTACCATCACACTT 57.771 39.130 0.00 0.00 38.50 3.16
2169 2316 3.933332 GGAGCAAGTAAGTACCATCACAC 59.067 47.826 0.00 0.00 0.00 3.82
2183 2330 0.109342 CACCAACCAGAGGAGCAAGT 59.891 55.000 0.00 0.00 0.00 3.16
2191 2338 0.179048 TGCAGACACACCAACCAGAG 60.179 55.000 0.00 0.00 0.00 3.35
2222 2391 8.424133 ACCATTTCAAGCTTATTTTCTGTTTCT 58.576 29.630 0.00 0.00 0.00 2.52
2288 2457 9.970395 TGATCTCATGGCATATGTTTTTATTTC 57.030 29.630 0.00 0.00 0.00 2.17
2293 2462 9.321562 GAATTTGATCTCATGGCATATGTTTTT 57.678 29.630 0.00 0.00 0.00 1.94
2362 2531 4.960938 TGACTCAATAGAACAGTGTGCTT 58.039 39.130 9.65 0.00 0.00 3.91
2393 2562 1.340088 ATGTGCAAAGTGCCCATCAA 58.660 45.000 0.00 0.00 36.80 2.57
2429 2598 7.015974 AGAGAAGAGTTGGACATATGCATATGA 59.984 37.037 40.23 23.16 42.05 2.15
2593 2763 1.808411 ACATCACCGAACTCGCATTT 58.192 45.000 0.00 0.00 38.18 2.32
2641 2811 3.117663 AGGGTTTAAGTTTCCACAGCTCA 60.118 43.478 0.00 0.00 0.00 4.26
2647 2817 4.330250 GAGGGTAGGGTTTAAGTTTCCAC 58.670 47.826 0.00 0.00 0.00 4.02
2767 2937 1.202687 CCAGTCAGAGCAAAGACCACA 60.203 52.381 0.00 0.00 35.38 4.17
2851 3021 1.071542 TGAACCTCGCCATTGAACTCA 59.928 47.619 0.00 0.00 0.00 3.41
2869 3039 5.072736 AGCCATATCTGTGATGAGGAATTGA 59.927 40.000 0.00 0.00 0.00 2.57
2872 3042 6.887886 ATAGCCATATCTGTGATGAGGAAT 57.112 37.500 0.00 0.00 0.00 3.01
2953 3123 7.175467 TGCACATCAGTATCTTTGTTGAAATCT 59.825 33.333 0.00 0.00 0.00 2.40
2995 3165 4.339748 TGTAAGCATGAAGGCCAACAATA 58.660 39.130 5.01 0.00 0.00 1.90
3259 3429 2.766400 GGAGAGGTCGGAGCTCACG 61.766 68.421 31.79 16.35 44.69 4.35
3301 3471 2.230940 GCCCATCATCACGTCGACG 61.231 63.158 34.58 34.58 46.33 5.12
3304 3474 2.202743 ACGCCCATCATCACGTCG 60.203 61.111 0.00 0.00 32.37 5.12
3307 3477 2.186644 TGGACGCCCATCATCACG 59.813 61.111 0.00 0.00 37.58 4.35
3541 3711 0.396811 ACTCGAACCCCTTGTGGAAG 59.603 55.000 0.00 0.00 35.39 3.46
3723 3896 4.967036 AGAAGAGAAGAAGGGTGAAACAG 58.033 43.478 0.00 0.00 39.98 3.16
3733 3906 9.846248 CTAGAGAAGAAAAGAGAAGAGAAGAAG 57.154 37.037 0.00 0.00 0.00 2.85
3919 4100 2.809119 CAATACGGCAACAGGTGTACAA 59.191 45.455 0.00 0.00 0.00 2.41
3964 4145 0.818296 ACTGACCTGATCACTACGCC 59.182 55.000 0.00 0.00 32.37 5.68
3969 4150 2.455557 CTCCTCACTGACCTGATCACT 58.544 52.381 0.00 0.00 32.37 3.41
3998 4179 1.810532 CTCGGTGTCAGTAGGCCTC 59.189 63.158 9.68 0.21 0.00 4.70
4167 4349 4.142182 CCTCACCAGCAAAAACTGAAAAGA 60.142 41.667 0.00 0.00 40.25 2.52
4271 4486 6.090763 GTCAACCAACTTCAAAAACTTCCAAG 59.909 38.462 0.00 0.00 0.00 3.61
4273 4488 5.245075 AGTCAACCAACTTCAAAAACTTCCA 59.755 36.000 0.00 0.00 0.00 3.53
4274 4489 5.720202 AGTCAACCAACTTCAAAAACTTCC 58.280 37.500 0.00 0.00 0.00 3.46
4311 4526 4.057432 GCCAACAACAAAACATATGTGCT 58.943 39.130 9.63 0.00 0.00 4.40
4333 4548 6.819146 GGAAGAGGGTTATTTGAGTTGACTAG 59.181 42.308 0.00 0.00 0.00 2.57
4483 4706 4.148825 ATCGCTGGGTGACGGAGC 62.149 66.667 0.00 0.00 34.14 4.70
4484 4707 2.202797 CATCGCTGGGTGACGGAG 60.203 66.667 0.00 0.00 0.00 4.63
4485 4708 3.770040 CCATCGCTGGGTGACGGA 61.770 66.667 0.00 0.00 39.04 4.69
4493 4716 0.107017 ATTTCACTCCCCATCGCTGG 60.107 55.000 0.00 0.00 42.73 4.85
4494 4717 1.303309 GATTTCACTCCCCATCGCTG 58.697 55.000 0.00 0.00 0.00 5.18
4495 4718 0.181350 GGATTTCACTCCCCATCGCT 59.819 55.000 0.00 0.00 0.00 4.93
4496 4719 0.181350 AGGATTTCACTCCCCATCGC 59.819 55.000 0.00 0.00 35.79 4.58
4497 4720 1.475751 CCAGGATTTCACTCCCCATCG 60.476 57.143 0.00 0.00 35.79 3.84
4498 4721 1.566231 ACCAGGATTTCACTCCCCATC 59.434 52.381 0.00 0.00 35.79 3.51
4499 4722 1.285962 CACCAGGATTTCACTCCCCAT 59.714 52.381 0.00 0.00 35.79 4.00
4500 4723 0.698238 CACCAGGATTTCACTCCCCA 59.302 55.000 0.00 0.00 35.79 4.96
4501 4724 0.681243 GCACCAGGATTTCACTCCCC 60.681 60.000 0.00 0.00 35.79 4.81
4502 4725 0.681243 GGCACCAGGATTTCACTCCC 60.681 60.000 0.00 0.00 35.79 4.30
4503 4726 0.329596 AGGCACCAGGATTTCACTCC 59.670 55.000 0.00 0.00 35.37 3.85
4504 4727 1.815003 CAAGGCACCAGGATTTCACTC 59.185 52.381 0.00 0.00 0.00 3.51
4505 4728 1.548582 CCAAGGCACCAGGATTTCACT 60.549 52.381 0.00 0.00 0.00 3.41
4506 4729 0.890683 CCAAGGCACCAGGATTTCAC 59.109 55.000 0.00 0.00 0.00 3.18
4507 4730 0.899717 GCCAAGGCACCAGGATTTCA 60.900 55.000 6.14 0.00 41.49 2.69
4508 4731 0.613012 AGCCAAGGCACCAGGATTTC 60.613 55.000 14.40 0.00 44.88 2.17
4509 4732 0.613012 GAGCCAAGGCACCAGGATTT 60.613 55.000 14.40 0.00 44.88 2.17
4510 4733 1.000396 GAGCCAAGGCACCAGGATT 60.000 57.895 14.40 0.00 44.88 3.01
4511 4734 2.679716 GAGCCAAGGCACCAGGAT 59.320 61.111 14.40 0.00 44.88 3.24
4517 4740 1.451028 CTAGCTGGAGCCAAGGCAC 60.451 63.158 14.40 6.94 44.88 5.01
4518 4741 0.617535 TACTAGCTGGAGCCAAGGCA 60.618 55.000 14.40 0.00 44.88 4.75
4519 4742 0.105778 CTACTAGCTGGAGCCAAGGC 59.894 60.000 3.17 2.02 43.38 4.35
4520 4743 0.755686 CCTACTAGCTGGAGCCAAGG 59.244 60.000 3.17 0.00 43.38 3.61
4521 4744 1.490574 ACCTACTAGCTGGAGCCAAG 58.509 55.000 3.17 0.00 43.38 3.61
4522 4745 2.667470 CTACCTACTAGCTGGAGCCAA 58.333 52.381 3.17 0.00 43.38 4.52
4523 4746 1.133450 CCTACCTACTAGCTGGAGCCA 60.133 57.143 3.17 0.00 43.38 4.75
4593 4816 2.096174 CAGAAGACCGACTCGAAGGTAG 59.904 54.545 6.84 0.00 41.51 3.18
4664 4887 3.432326 GGCAGGAATCTATGTCGGAACTT 60.432 47.826 0.00 0.00 0.00 2.66


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.